Methane-eating microbes make their own oxygen

Bacteria may have survived on Earth without plants, thanks to unique metabolism.

Researchers have discovered a possible new species of bacteria that survives by producing and 'breathing' its own oxygen.
The finding suggests that some microbes could have thrived without oxygen-producing plants on the early Earth — and on other
planets — by using their own oxygen to garner energy from methane (CH4).

"The mechanism we have now discovered shows that, long ago, these organisms could have exploited the methane sources on Earth
and possibly on other planets and moons by mechanisms that we didn't know existed," says Mike Jetten, a microbiologist at
Radboud University Nijmegen in the Netherlands and part of the team that conducted the study, which is published in Nature today1.

The oxygen-producing bacterium, provisionally named Methylomirabilis oxyfera, grows in a layer of methane-rich but oxygen-poor mud at the bottom of rivers and lakes. The microbes live on a diet of methane
and nitrogen oxides, such as nitrite and nitrate. These nitrogen-containing compounds are especially abundant in sediment
contaminated by agricultural runoff.

Before the discovery of these bacteria, organisms were known to produce oxygen through only three chemical pathways: photosynthesis,
bacterial reduction of chlorates (ClO3– and ClO4–) and the enzymatic conversion of reactive oxygen species.

Now, Jetten and his colleagues have described a fourth pathway, in which microbes extract energy from methane through a chemical
process linked to denitrification, which releases nitrogen and oxygen from nitrogen oxides. The two known groups of methane-consuming
bacteria live in either the absence of oxygen (anaerobic methanotrophs) or exploit oxygen from the atmosphere (aerobic methanotrophs).
But M. oxyfera can survive in methane-rich areas that are inhospitable to many other bacteria. It does this with the help of an enzyme,
perhaps a nitric oxide dismutase, that combines two molecules of nitric oxide to form nitrogen and oxygen. The oxygen is then
used to metabolize methane to produce water and carbon dioxide.

"It's a very unusual form of metabolism in that it's not directly utilizing oxygen from photosynthesis," says David Valentine,
a geomicrobiologist at the University of California in Santa Barbara, who was not involved with the study. "It's an anaerobic
form of metabolism at heart that then produces oxygen and becomes an aerobic form of metabolism."

Strange brew

Scientists have long suspected that some microbes might be capable of oxidizing methane by converting nitrogen oxides to
atmospheric nitrogen. But until recently, no one had successfully grown such microbes in the laboratory. In a 2006 study,
this team demonstrated for the first time that anaerobic methane oxidation could be coupled to nitrogen oxide reduction2.

“It's an anaerobic form of metabolism at heart that then produces oxygen and becomes an aerobic form of metabolism.”

For the latest study, the researchers gathered a bucket of mud from a local ditch and coaxed the microbes into growing inside
glass vessels, devoid of oxygen, by adding small amounts of nitrite from minerals dissolved in water and bubbling the culture
with methane. After about six months, they managed to get enough bacteria to grow in the mud for further study.

The team then sequenced the genome of the dominant organism in the mud, M. oxyfera, and compared it with other bacteria that are known to dine on methane or produce nitrogen gas. "It was very paradoxical,"
says Katharina Ettwig, a PhD student in microbiology and an author of the paper. "We found that they did have all the pathways
that are necessary for living with oxygen, although they never see any oxygen, at least in our culture."

Which came first?

The order of evolution of metabolic pathways on the early Earth is still hotly debated. Numerous enzymes exist that use oxygen
but seem to pre-date the actual presence of oxygen on Earth from photosynthesis, says Ettwig. One possible explanation for
this is that these enzymes did not originally use oxygen, but rather nitric oxide, which would require a similar metabolic
pathway. "We add another possibility to this debate — that some microorganisms could have produced their own oxygen," says
Ettwig.

The discovery of this new pathway also has implications for life on Mars, where methane exists as a trace gas in the atmosphere,
and on Titan, Saturn's largest moon, where there are shallow pockets of liquid methane. In such environments, alien microbes
could use this pathway to live off the carbon and energy supplied by methane, says Ronald Oremland, a microbiologist specializing
in geochemistry with the US Geological Survey in Menlo Park, California.

Valentine says that the finding may be followed by the discovery of other novel metabolic pathways. "When we look at the organisms
that exist in nature, there are so many that we can identify by some molecular signature, but we have yet to figure out what
they're actually doing, how they acquire their energy and what their lifestyles are," he says.

Oremland adds that the study introduces numerous questions of evolutionary significance that can only be answered through
further studies. "We need to figure out who came first — aerobic methanotrophs that we've studied for so long and know so
much about, or these guys?" The study also raises another possibility: that these microbes arose much later and that they
are thriving due to the presence of nitrate- and methane-rich environments caused by human activity. "Is that possible? Who
knows. Only more studies will answer those larger questions," he says.